Bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency.


Sentieon provides complete solutions for secondary DNA analysis. Its software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines. The Sentieon tools are deployable on any generic-CPU-based computing system. Sentieon products are already installed at over 100 sites worldwide. Its products have been extensively tested and validated by numerous customers, and have run through tens of thousands of genome datasets, the majority of which are WGS or WES, with a total of over 2 peta-basepairs of DNA.
  • Sentieon DNAseq
    Sentieon DNAseq implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.x Best Practice Workflow pipeline, but with more efficient computing algorithms and enterprise-strength software implementation. Compared to the BWA-GATK pipeline, the Sentieon DNAseq pipeline is 10X faster measured in terms of total core hours for processing from FASTQ to VCF, on the same generic-CPU-based system with no special hardware requirements. This includes a computing efficiency enhancement to BWA-MEM. For aligned-BAM-to-VCF processing, Sentieon DNAseq is 20X-50X faster than GATK. The software is also able to do joint call on over 100K samples together without intermediate file merging, saving time and effort.
    • Identical mathematics as Broad Institute’s BWA-GATK Best Practice Workflow, but over 10X faster FASTQ-to-VCF, 20X-50X faster BAM-to-VCF, measured in core-hours
    • No run-to-run difference, no down-sampling in high coverage regions
    • 100K samples joint-calling without intermediate file merging
    • Pure software solution running on any generic-CPU-based system
  • Sentieon TNseq
    Sentieon TNseq is a tumor-normal pair somatic variant detection product with modes that can match either MuTect (calls SNV in somatic variants) or MuTect2 (MuTect2 is currently in beta release by the Broad Institute; it calls both SNV and INDEL in somatic variants) in the same sense as Sentieon DNAseq matches BWA-GATK: identical mathematics, but more efficient computing algorithms and enterprise-strength software implementation.
    • Identical mathematics as Broad Institute’s Mutect and MuTect2, but over 10X faster FASTQ-to-VCF, measured in core-hours
    • No run-to-run difference, no down-sampling in high coverage regions
    • Pure software solution running on any generic-CPU-based system

Use Cases

Align & Variant Calling

Sentieon’s secondary analysis pipeline has proven to be powerful to call single nucleotide variations and INDELs for germline and cancer data...

It provides significant speed advantages over existing methods, without sacrificing precision and accuracy. Sentieon’s products are highly synergistic with Golden Helix Copy Number Caller VS-CNV. The two products combined provide the most complete secondary analysis solution in the industry. While this solution will benefit all of our users, we are particularly excited for our customers that operate in a high-throughput environment.

Recommended Learning Materials

We have a variety of supplemental learning materials that are an excellent resource for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VarSeq!


Check out our free eBooks on a variety of different topics:

Other Resources

Learn more about Sentieon by checking out these informative whitepapers!

Try Sentieon for Free

Did you know we offer complimentary trials of our software? No restricted features, no sample data - you get to try all the features of Sentieon with your data and see how it works!

If you are interested in a trial, please fill out the form below, and we will send you the details!

Technical Specifications

VarSeq is on-premises software, ensuring full control over installation and data management. It is compatible with various deployment environments including workstations, server setups with remote desktop access, and private cloud servers.

The software is optimized for operation within strict corporate firewalls. It seamlessly integrates with existing web proxy configurations, ensuring uninterrupted functionality in secured network infrastructures. VarSeq's internet connectivity requirements are minimal. It only needs to connect to a select group of Golden Helix servers. This connection is essential for license verification and accessing annotation data updates.

See System Requirements for more details of hardware and operating systems requirements based on planned workflows.